[Openmd-users] Streptavidin on biotinylated gold nano-particle

[Dan Gezelter]

Dear Mohammad,

  Creating and simulating biotin / streptavidin is possible - if you have built OpenMD with the openbabel library, you can use the included atom2md program to convert to MD format:

atom2md -ipdb 1STP.pdb -omd 1STP.md -h

This creates the initial input file using the PDB file for the streptavidin / biotin complex and protonates the structure.  N.B. some of the added hydrogens (e.g. for GLU residues) are probably incorrect.  This will need significant cleanup.  If you have a structure for the isolated biotin molecule, you can create a simple test case:

atom2md -ipdb biotin.pdb -omd biotin.md

I'm attaching a processed version of the coordinate and include files below.  Note that no force field or other parameters have been defined, so they won't really be usable until you define a force field.

When you use atom2md, the atom types are created assuming the Amber force field for proteins and generic hybridization-typed atoms for non-proteins. The primary difficulty with the project you've described is that there aren't particularly good models for the cross interactions between the metallic gold nanoparticle and charged atom types like the ones in use in Amber (and I think biotin also needs some special handling in the Amber force field).  The force fields for metals (e.g. EAM and Sutton-Chen) don't include metallic polarization, so you'd be missing important components of the interaction between the various protein / ligand molecules and the particles.

If there are parametrized force fields that you know you want to use, we can help you set those up.  

Best regards,

 --Dan Gezelter


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> On Nov 20, 2014, at 9:30 PM, Mohammad Mahdi Salary Shahrbabaki <salaryshahrbabaki.m at husky.neu.edu> wrote:
> 
> Dear Professor Gezelter,
> 
> I am quite naive about molecular dynamics but I need to simulate binding of streptavidin molecules to a 20 nm sized biotinylated gold nano-particle for my work. I have built the gold nano-particle using the instructions in the website. Now I need to add biotin ligands into gold nano-particle and then determine the binding sites of streptavidin on the surface of biotinylated particle. I was wondering if it is possible to do all of these simulations using OpenMD? 
> 
> I would greatly appreciate any help and suggestions you could provide.
> 
> Best,
> Mohammad
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> Openmd-users mailing list
> Openmd-users at openmd.org
> http://openmd.org/mailman/listinfo.cgi/openmd-users

***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************